Fullerene and 3D molecules are not represented as 3D in the Miew 3D window

[baranovdv]

Steps to Reproduce

1. Open CDX file from ChemDraw (Fullerene and 3D molecules)
   

2. Ketcher Mview
   

Actual behavior
Fullerene and 3D molecules are not represented as 3D in the Miew 3D window.
Kindly see pictures.
Task epam/ketcher#4232

Expected behavior
Fullerene and 3D molecules should be represented as 3D in the Miew 3D window.

Attachments
FullereneCDX-example.zip

Related:

• Fullerene and 3D molecules are not represented as 3D in the Miew 3D window ketcher#4291

Environment details:
• OS: Windows 10 Pro (version 22H2) x64
• Browser: Сhrome
• Version: (122.0.6261.95) x64

Ketcher version 2.19.0 – rc.2
Indigo Toolkit
Version 1.18.0-rc.6.0-g98bf384e0-x86_64-linux-gnu-11.2.1

Additional context:
When converting from .cdx to .ket Indigo should return atoms with correct z-coordinate

[AlexeyGirin]

See epam/ketcher#4291 for extra details (in comments)

[gilvan-fernandes]

Hello

My team is considering Ketcher, and this fix would add up a lot to make our case convincing our stakeholders. Is there a prediction about when this will be available? At least in a release candidate?

[rrodionov91]

Hi @gilvan-fernandes

Thank you for feedback.

It was fixed on Ketcher side in this ticket epam/ketcher#3501 in 2.22.0-rc.2. We are going to make public release 2.22.0 soon, however you can use 2.22.0-rc.9, it is stable.

[gilvan-fernandes]

Thank you for the fast response!

[rrodionov91]

Z coordinate in KET format fixed on Ketcher side in epam/ketcher#3501
However it is removed after CDX/CDXML conversion by indigo.
@gilvan-fernandes it works for KET, MOL V2000, MOL V3000 formats, but not for CDX/CDXML. Fix for it planned in Indigo 1.23.0-rc.1 (Ketcher 2.24.0-rc.1)

[AlexeyGirin]

No fixed.
Still flat.

• Ketcher Version 2.23.0-rc.3 Build at 2024-07-31; 05:31:01
• Indigo Toolkit Version 1.23.0-dev.2.1-gd93b8ec4-wasm32-wasm-clang-12.0.0
• Windows 10 Pro
• Chrome Version 127.0.6533.89 (Official Build) (64-bit)

[AlexeyGirin]

Fixed.
Provided cdx doesn't contain z-coordinates and ChemDraw uses it's own capabilities to create them from the scratch.
I created my own cdx (3d structures example.zip) with z-coordinates in place and it works correct in both - ChemDraw and Ketcher

• Ketcher Version 2.23.0-rc.3 Build at 2024-07-31; 05:31:01
• Indigo Toolkit Version 1.23.0-dev.2.1-gd93b8ec4-wasm32-wasm-clang-12.0.0
• Windows 10 Pro
• Chrome Version 127.0.6533.89 (Official Build) (64-bit)